QC Scatter Plot — QCPlot • phenoscapR

Scatter plot of two QC metrics (e.g. cell area vs total intensity).

Usage

QCPlot(object, x, y, colour_by = NULL, pt_size = 0.5)

Arguments

object: An SpatialCellData object.
x: Character. Metadata column for x-axis.
y: Character. Metadata column for y-axis.
colour_by: Character or NULL. Metadata column for colour.
pt_size: Numeric. Default 0.5.

Value

A ggplot object.

Examples

counts <- matrix(rnorm(100), nrow = 50,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(50), y = runif(50))
meta <- data.frame(cell_id = 1:50, sample_id = "s1",
                   cell_area = runif(50, 10, 500))
obj <- CreateSpatialObject(counts, coords, meta)
QCPlot(obj, x = "cell_area", y = "cell_id")